X Region Profile Normalize

Image : Image

A filter which normalises the data frame by the profile of the selected region of the X axis.

Options

Smoothing Width : Smoothing amount of the integrated line

X Range : Range in X direction (i.e. 10,20)

Standard Normal Variate

XY : XY

Subtract mean and divide by standard deviation to bring all XY data onto the same scale

Options

Set Poisson Error [Error]

Image : Image

Sets the current value of the data as the variance on the dataset

Options

ARPES Gold Calibration Correction [ARPES Analysis]

Image : Image

ARPES Gold Calibration Correction

Options

Calibration File : Path to the calibration NeXus file

energyOffset :

ARPES Axis Conversion [ARPES Analysis]

Image : Image

ARPES Axis Conversion

Options

kxOffset :

kyOffset :

workFunction :

Crop Data [1D]

XY : XY

Crop XY data to a specified range

Options

Start : Set beginning of range to crop data to

Stop : Set end of range to crop data to

Average All Data

Any : Same

Average all the data into a single dataset

Options

Crop Data [2D]

Image : Image

Crop an image to a specified size

Options

X Start : Lower bound of crop in X-direction

X Stop : Upper bound of crop in X-direction

Y Start : Lower bound of crop in Y-direction

Y Stop : Upper bound of crop in Y-direction

Mask Outside Region [Masking]

Image : Image

Mask pixels outside the specified region

Options

Region of Interest : Define the region of interest

Normalisation [External Data]

Any : Same

Normalise data against the value from a corresponding value in an external dataset (if path is empty, dataset from processed file is used)

Options

File : Enter the path to the data file, leave blank to use the file being processed

Dataset : Enter the name of the dataset to be used

Subtract Data [External Data]

Any : Same

Subtract a dataset (or average if stack) in the specified file

Options

File : Enter the path to the data file

Dataset :

First: : Position of first (or only) dataset, leave blank to average all data

Last: : Position of end dataset, leave empty to use a single dataset

Scaling : Scaling of the multiplying data

Diffraction Ellipse Fit [XRD2 Image Processing]

Image : Image

Fit an ellipse to the ring at the specified q value - parameters returned as auxiliary data

Options

Ellipse q : Value of q the ellipse corresponds to

q delta : The range of q to search for the ellipse in

Image Rotation

Image : Image

Rotates an image by a certain angle around the image centre

Options

Angle : The image will be rotated by the angle provided around the centre of the dataset (x=xMax/2, y=yMax/2)

Resize : Resize resulting bounding box

Unit : Angle unit

Affine Transformation

Image : Image

Performs an affine transformation on the image

Options

a11 :

a12 :

a21 :

a22 :

dx :

dy :

Resize : Resize resulting bounding box

Convert Diffraction Axis Type [1D]

XY : XY

Convert XY diffraction data axes between q, 2 theta and d-space

Options

Use Calibrated Wavelength : Use wavelength from detector calibration.

Wavelength : Specify a wavelength to use.

X Axis : Set value for X axis after integration

Rebin XY Data

XY : XY

Rebin data onto new axis with specified start, stop and number of points (defaults to min, max and number of points in first axis

Options

Max : Maximum value to use in rebinning, leave blank to use the max from the first dataset

Min : Minimum value to use in rebinning, leave blank to use the min from the first dataset

Number of bins : Number of bins to rebin the data into, leave blank to use the number of bins from the first dataset

Iterative Polynomial Baseline Subtraction [Background Subtraction]

XY : XY

Subtract a polynomial baseline using an iterative fitting routine. On each iteration any data above the fit is set to the fit value.

Options

Number of Iterations : Number of iterations to use in fitting process

Polynomial Order : Polynomial orde to use for baseline

Subtract Input Data

Any : Same

Subtract a selected dataset of the input data (or average) from all datasets

Options

First: : Position of first (or only) dataset, leave blank to average all data

Last: : Position of end dataset, leave empty to use a single dataset

Scaling : Scaling of the multiplying data

Average Fastest Dimension Only

Any : Same

Averages the data along the fastest non-data dimension of the array. For example, if the data set shape is [a,b,c,X,Y] where X and Y are the data dimensions, c is the fastest axis (row-major order)

Options

Image Threshold [Image Filter]

Image : Image

Applies a threshold across the whole image

Options

Down : If 'down' is true, then pixels with values <= to 'threshold' are set to 1 and the others set to 0. If 'down' is false, then pixels with values >= to 'threshold' are set to 1 and the others set to 0.

Radius : Used for adaptive thresholding algorithms that are computed using a local square region centered on each pixel.

Threshold : Value used for GLOBAL_CUSTOM thresholding

Type : Type of thresholding algorithm

Blob Extraction [Binary Image]

Image : Image

Extracts blobs on binary image

Options

Connect Rule : Connectivity rule: blobs can be defined using a 4 or 8 connect rule

Image Stitching [External Data]

Image : Image

Stitches two images together given X and Y translations

Options

File : Enter the path to the data file, leave blank to use the file being processed

Dataset Name : The name of the dataset or the node path of the data if a .NXS file

X Translation : X translation between two images in pixels

Y Translation : Y translation between two images in pixels

Dataset Concatenation [External Data]

Image : Image

Concatenate two datasets together, taking into account axes scaling

Options

File : Enter the path to the data file, leave blank to use the file being processed

Dataset name : Dataset name (leave empty to use input dataset name

Concatenation axis : The axis along which the concatenation will occur

General Detector Error [Error]

Image : Image

Options

No Data [Utilities]

Any : Same

Stops data being sent down the pipeline, used to not duplicate your data if you only need the auxiliary output

Options

No Change [Utilities]

Any : Same

Propagates the input data without modifying it, used to convert other data formats to nexus

Options

Export to Text File [Image]

Image : Image

Save image as text with x axis as first column, use with caution, files can get very large

Options

File Extension : Extension that should be used for the output file

Include explicit location : Include the explicit (slice) location of the data in the full dataset as part of the filename

Output Directory : Path to output directory

Pad with zeros : Leave blank for no padding

Suffix : Custom suffix to be appended to the file name, leave blank for no suffix

Average Sections of Fastest Dimension

Any : Same

Averages sections of the data along the fastest non-data dimension of the array. For example, if the data set shape is [a,b,c,X,Y] where X and Y are the data dimensions, c is the fastest axis (row-major order)

Options

number :

start :

stop :

Centroid

Image : Image

Determine the X and Y centroid values (saved to file)

Options

Minimum Maximum Normalization

XY : XY

Normalize the minimum to zero and the maximum to one

Options

Pseudo-Flat Field Filter [Image Filter]

Image : Image

Creates a Gaussian-blurred image using the given kernel and then subtract the blurred image/pseudo flat field from the original image

Options

Kernel Width : Width of filter kernel in pixels

Spline Baseline Subtraction [Background Subtraction]

XY : XY

Subtract a spline from the data

Options

Control point x-values : Enter a list of comma-separated x values for the spline control points.

Image Integration

Image : XY

Integrate an image along a selected axis

Options

Direction of Profile : The direction to see the profile in.

Do average? : Average the data along the chosen axis, rather than sum.

Normalisation [metadata]

Any : Same

Divide data by a value taken from the file metadata

Options

metadataName :

Multiply [External Data]

Any : Same

Multiply dataset by external value

Options

File : Enter the path to the data file, leave blank to use the file being processed

Dataset : Enter the name of the dataset to be used

Subtract [External Data]

Any : Same

Subtract external data from a dataset

Options

File : Enter the path to the data file, leave blank to use the file being processed

Dataset : Enter the name of the dataset to be used

Divide [External Data]

Any : Same

Divide dataset by external value

Options

File : Enter the path to the data file, leave blank to use the file being processed

Dataset : Enter the name of the dataset to be used

Add [External Data]

Any : Same

Add external data to a Dataset

Options

File : Enter the path to the data file, leave blank to use the file being processed

Dataset : Enter the name of the dataset to be used

Two Box Mean Difference

Image : Image

Difference between the mean of two boxes

Options

Box 1 : Define the first region of interest

Box 2 : Define the second region of interest.

Two Box Mean Ratio

Image : Image

Ratio of the mean of two boxes

Options

Box 1 : Define the first region of interest

Box 2 : Define the second region of interest.

Mask by coordinate [Masking]

Image : Image

Mask values inside, or outside a set co-ordinate range

Options

Coordinate : Set coordinate for to mask over

Mask range? : Mask over the range when checked, outside the range otherwise

Range : Please set two values, start and end, separated by a comma i.e. 2,4. The values should match the coordinate selected (i.e. q, 2 theta, pixel).If you delete the text, the range is cleared and the whole image used.

Read Nexus Detector Information

Image : Image

Read calibration and mask from the NeXus file being processed

Options

readGeometry :

readMask :

Fit Imported Function

XY : XY

Fit a function to the data, using a function generated in the function fitting tool and exported as a NeXus file

Options

Function File : Enter the path to the function file

optimiser :

Multiply by Scalar

Any : Same

Multipy by a scalar

Options

value :

Subtract Scalar

Any : Same

Subtract a scalar

Options

value :

Divide by Scalar

Any : Same

Divide by a scalar

Options

value :

Add Scalar

Any : Same

Add a scalar

Options

value :

Box Mean

Image : Image

Returns mean values within a Box

Options

Box : Define the region of interest.

Subtract Average X Regions Integration

Image : XY

Subtract the average of two regions in X from the signal region

Options

Set background 1 range : Please set two values, start and end, separated by a comma, for example 2,4. The values should match the axis . If you delete the text, the range is cleared and the whole range used.

Set background 2 range : Please set two values, start and end, separated by a comma, for example 2,4. The values should match the axis . If you delete the text, the range is cleared and the whole range used.

Set signal range : Please set two values, start and end, separated by a comma, for example 2,4. The values should match the axis . If you delete the text, the range is cleared and the whole range used.

Multiply [Internal Data]

Any : Same

Multiply dataset by internal value

Options

Dataset : Enter the name of the dataset to be used

Subtract [Internal Data]

Any : Same

Subtract internal data from a dataset

Options

Dataset : Enter the name of the dataset to be used

Divide [Internal Data]

Any : Same

Divide dataset by internal value

Options

Dataset : Enter the name of the dataset to be used

Add [Internal Data]

Any : Same

Add internal data to a Dataset

Options

Dataset : Enter the name of the dataset to be used

Multiply Frame [External Data]

Any : Same

Multiply dataset by frame (or average of stack) from external file

Options

File : Enter the path to the data file

Dataset :

First: : Position of first (or only) dataset, leave blank to average all data

Last: : Position of end dataset, leave empty to use a single dataset

Scaling : Scaling of the multiplying data

Subtract Frame [External Data]

Any : Same

Subtract frame (or average of stack) from external file

Options

File : Enter the path to the data file

Dataset :

First: : Position of first (or only) dataset, leave blank to average all data

Last: : Position of end dataset, leave empty to use a single dataset

Scaling : Scaling of the multiplying data

Divide Frame [External Data]

Any : Same

Multiply dataset by frame (or average of stack) from external file

Options

File : Enter the path to the data file

Dataset :

First: : Position of first (or only) dataset, leave blank to average all data

Last: : Position of end dataset, leave empty to use a single dataset

Scaling : Scaling of the multiplying data

Add Frame

Any : Same

Add frame (or average of stack) from external file

Options

File : Enter the path to the data file

Dataset :

First: : Position of first (or only) dataset, leave blank to average all data

Calibration data path is default path (It) : If true, calibration data will be extracted from the default location, /entry1/It/data. If false, data will be from the calibration data location defined here

Calibration file : File containing calibration data

Calibration file is current data file : If true, calibration data will be extracted from the current data file. If false, data will be from the calibration file defined here

Thickness in file is default : The thickness value in the file at /entry1/sample/thickness is default. If false, use the thickness value in defined here

XPDF Azimuthal Integration [XPDF beta]

Image : XY

Options

Azimuthal range : Please set two values, start and end, separated by a comma i.e. -90,90, maximum range is 360

Number of bins : Set number of bins for integration axis, leave blank for maximum pixel distance on detector

Pixel splitting :

Radial range : Please set two values, start and end, separated by a comma i.e. 2,4.The values should match the axis selected (i.e. q, 2 theta, pixel).If you delete the text, the range is cleared and the whole image used.